A better way to composite one video sub-clip over another with chroma key?
You are right, you would:
1. use the chroma key source as a single input node then generate a key with the keyer node. This scene will appear in the VSE as a strip with an alpha channel


add an Alpha Convert node set to "Straight to Premultiplied"
Add the scene strip to the VSE timeline on top of the background strip. Check its blend type and make it "alpha over" instead of cross or replace.


You should then be able to trim it to length as required. Remember that to get audio you would have to add the original source strip to the VSE timeline of the compositor scene. But this only works in the latest versions of Blender.

Otherwise you will have to sync the sound up to the scene strip.